DNA methylation as a therapeutic target in RB1 deficient and neuroendocrine prostate cancer and rational co-targeting with B7-H3
DNA methylation · human · 31 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Topic
- Prostate cancerThis series is part of our curated briefing on it.
- Samples
- 31 samples: 8 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Targeting DNA methylation and B7-H3 in RB1-deficient and neuroendocrine prostate cancerScience translational medicine · 2023
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE216054_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA891770 and SRA study SRP403293. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 16 samples read as cases, 15 as controls.
How we read this: 8 replicated groups read from 31 sample titles; they account for 25 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM6657904 DNA methylation in PM154 control
- GSM6657905 DNA methylation in PM154 decitabine treated
- GSM6657906 DNA methylation in PM12 control
- GSM6657907 DNA methylation in 22Rv1 control
- GSM6657908 DNA methylation in 22Rv1 sgRB1 control
- GSM6657909 DNA methylation in 22Rv1 sgRB1 decitabine treated
- GSM6657918 PM154, Control, rep1 PM154, Control,
- GSM6657919 PM154, Control, rep2 PM154, Control,
- GSM6657920 PM154, Control, rep3 PM154, Control,
- GSM6657921 PM154, DNMT1 knockout, rep1 PM154, DNMT1 knockout,
- GSM6657922 PM154, DNMT1 knockout, rep2 PM154, DNMT1 knockout,
- GSM6657923 PM154, DNMT1 knockout, rep3 PM154, DNMT1 knockout,
- GSM6657924 PM154, DNMT3A knockout, rep1 PM154, DNMT3A knockout,
- GSM6657925 PM154, DNMT3A knockout, rep2 PM154, DNMT3A knockout,
- GSM6657926 PM154, DNMT3A knockout, rep3 PM154, DNMT3A knockout,
- GSM6657927 PM154, Control, rep1 PM154, Control,
- GSM6657928 PM154, Control, rep2 PM154, Control,
- GSM6657929 PM154, Control, rep3 PM154, Control,
- GSM6657930 PM154, decitaine treated, rep1 PM154, decitaine treate…
- GSM6657931 PM154, decitaine treated, rep2 PM154, decitaine treate…
- GSM6657932 PM154, decitaine treated, rep3 PM154, decitaine treate…
- GSM6689313 22Rv1, Control, rep1 22Rv1, Control,
- GSM6689314 22Rv1, Control, rep3 22Rv1, Control,
- GSM6689315 22Rv1, CD276 knockout, rep1 22Rv1, CD276 knockout,
- GSM6689316 22Rv1, CD276 knockout, rep3 22Rv1, CD276 knockout,
- GSM6689317 22Rv1, WT-1 22Rv1, WT
- GSM6689318 22Rv1, WT-2 22Rv1, WT
- GSM6689319 22Rv1, WT-3 22Rv1, WT
- GSM6689320 22Rv1, RB1 knockout-1 22Rv1, RB1 knockout
- GSM6689321 22Rv1, RB1 knockout-2 22Rv1, RB1 knockout
- GSM6689322 22Rv1, RB1 knockout-3 22Rv1, RB1 knockout
- GSE115501 RNA sequencing on circulating tumor cells from prostate cancer patients 136 samples same disease briefing · shares prostate
- GSE222467 The RNA binding proteins LARP4A and LARP4B promote tumour growth and metastasis in prostate cancer and osteosarcoma 12 samples same disease briefing · shares prostate
- GSE300947 A novel six-biomarker panel identified from male breast cancer-associated fibroblasts demonstrates prognostic power for prostate tumors 6 samples same disease briefing · shares prostate
- GSE120181 Human prostate cancer cell line, 22Rv1: Control vs. luteolin treatment 2 samples same disease briefing · shares prostate
- GSE71008 Plasma extracellular RNA profiles in healthy and cancer patients 192 samples same disease briefing
- GSE242541 ONECUT2 is a druggable driver of luminal to basal breast cancer plasticity 12 samples same disease briefing
- GSE216713 DNA methylation as a therapeutic target in RB1 deficient and neuroendocrine prostate cancer and rational co-targeting with B7-H3 [22Rv1sgRB1] 6 samples shares b7-h3, rb1, neuroendocrine, co-targeting, methylation, therapeutic, deficient, prostate
- GSE328076 LHX2 drives neuroendocrine transformation in TP53/RB1-deficient prostate cancer 14 samples shares rb1, neuroendocrine, deficient, prostate
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.